EBC Rotors and tolerances

Hey, guys, I got my first ride of the...... day, today! :) (I have
about 1500 miles so far this year, give or take.)
So anyway, by sheer negligence, I failed to notice how worn the pads
were on my wife's Ninjette (250) rear brake, and it thoroughly trashed
the rotor. Really ugly!
So we ordered an EBC rotor to fit, from their basic "MD" line since
it's the only non-OEM rear rotor I can find for the Ninja 250
*anywhere*. After a fumble where the shop actually ordered a front
rotor, we did get a replacement rotor. (I've gotten rotors off ebay
before that were worse than the ones I wanted to replace, so I gave up
on that approach.)
So I did what I thought one was supposed to do, and went over the
rotor lightly & evenly with an orbital sander to knock off the glaze,
before installing it.
She rode it one day after that and said the pedal pulsed fairly
heavily, so I got out my trusty caliper (cuz I couldn't find my
less-trusty micrometer) and measured a variation of 4.42mm to 4.50mm,
on four evenly spaced spots on the rotor.
However, I'm not sure if that's within normal tolerances for a rotor,
does anyone know? I'm sure it's not given the amount of pulsing the
brake does.
I also wonder if I made a mistake in deglazing the rotor surface
before I installed it - I used the sander in smooth circles for about
10 seconds a side, using about 150-grit paper. I don't *think* that's
enough to remove 0.08mm of material on a side, but if I screwed this
up, then... I won't do it next time.
Whaddya all know?